# Please go to the end to see rules of defining an atom  

============================================================================================
                        Defination begin
============================================================================================
--------------------------------------------------------------------------------------------
WILDATOM XX C N O S P
WILDATOM XA O S
WILDATOM XB N P
WILDATOM XC F Cl Br I
-------------------------------------------------------------------------------------------- 
 f1  f2    f3  f4  f5  f6  f7  f8      			f9         	f10 
-------------------------------------------------------------------------------------------- 
ATD  CT    *   6   4   &                                    
ATD  C     *   6   3   *   *   *       	      	 	(XA1)			&
ATD  CN    *   6   3   *   *   [RG5,RG6,AR1.AR2.AR3]   	(C3,C3,N3(H))		&
ATD  CB    *   6   3   *   *   [RG5,RG6,AR1.AR2.AR3]    &
ATD  CR    *   6   3   *   *   [RG5,AR1.AR2.AR3]        (N3,N3)			&
ATD  CR    *   6   3   *   *   [RG5,AR1.AR2.AR3]        (N2,N3(H))		&
ATD  CK    *   6   3   *   *   [RG5,AR1.AR2.AR3]        (N2,N3) 		&	 
ATD  CC    *   6   3   0   *   [RG5,AR1.AR2.AR3]        (C3,N3(C3,H))		&
ATD  CC    *   6   3   0   *   [RG5,AR1.AR2.AR3]        (C3,N2(C3))		&
ATD  CW    *   6   3   *   *   [RG5,AR1.AR2.AR3]        (C3,N3(H))		&
ATD  CV    *   6   3   *   *   [RG5,AR1.AR2.AR3]        (C3,N2)			&
ATD  C*    *   6   3   *   *   [RG5,AR1.AR2.AR3]        (C3,C3)			&
ATD  CQ    *   6   3   *   *   [RG6,AR1.AR2.AR3]        (N2,N2)			&
ATD  CM    *   6   3   *   *   [RG6,AR1.AR2.AR3]        (C3,C3(N2(C3(N3(C3))))) &
ATD  CM    *   6   3   *   *   [RG6,AR1.AR2.AR3]        (C3,C3(N3(C3(N3(C3))))) &
ATD  CM    *   6   3   *   *   [RG6,AR1.AR2.AR3]        (C3,N3(C3(N2(C3(C3))))) &
ATD  CM    *   6   3   *   *   [RG6,AR1.AR2.AR3]        (N3,C3(C3(N3(C3(N3))))) &
ATD  CA    *   6   3   *   *   [AR1.AR2.AR3]             &	
ATD  CD    *   6   3   *   *   *                        (C3,C3)			& 
ATD  CM    *   6   3   &
ATD  CZ    *   6   2   &
ATD  H     *   1   1   *   *   *                        (N)			&
ATD  HO    *   1   1   *   *   *                        (O)			&
ATD  HS    *   1   1   *   *   *                        (S)			&
ATD  HP    *   1   1   *   *   *                        (C(N4))			&
ATD  HW    *   1   1   *   *   *                        (O(H1))			&
ATD  H3    *   1   1   *   3   *                        (C4)			&
ATD  H2    *   1   1   *   2   *                        (C4)			&
ATD  H1    *   1   1   *   1   *                        (C4)			&
ATD  HC    *   1   1   *   *   *                        (C4)			&
ATD  H5    *   1   1   *   2   *                        (XX[AR1.AR2.AR3])	&
ATD  H4    *   1   1   *   1   *                        (XX[AR1.AR2.AR3])	&
ATD  HA    *   1   1   *   *   *                        (XX[AR1.AR2.AR3])	&
ATD  HA    *   1   1   &
ATD  F     *   9   1   &
ATD  Cl    *   17  1   &
ATD  Br    *   35  1   &
ATD  F     *   53  1   &
ATD  P     *   15  &
ATD  N1    *   7   1   &   
ATD  NB    *   7   2   *   *   [RG5,AR1.AR2.AR3]         & 
ATD  NC    *   7   2   *   *   [RG6,AR1.AR2.AR3]         & 
ATD  N2    *   7   *   *   *   *                         (C3(N3,N3))		&
ATD  N2    *   7   *   *   *   *                         (C3(N3,N3))		&
ATD  NO    *   7   3   *   *   *                         (O1,O1)		&
ATD  NA    *   7   3   1   *   [RG5.RG6,AR1.AR2.AR3]     & 
ATD  N2    *   7   3   *   *   [NR]                      (XX[AR1.AR2.AR3]) 	&
ATD  N*    *   7   3   *   *   [AR1.AR2.AR3]             &
ATD  N     *   7   3   *   *   *                         (C3(XA1))		&
ATD  NT    *   7   3   &   
ATD  N3    *   7   4   &   
ATD  O2    *   8   1   *   *   *                         (C(O1))		&
ATD  O2    *   8   1   *   *   *                         (P)			&
ATD  O     *   8   1   *   *   *                         (C)			&
ATD  O     *   8   1   *   *   *                         (S)			&
ATD  OH    *   8   2   1   & 
ATD  OW    *   8   2   2   & 
ATD  OS    *   8   2   & 
ATD  SH    *   16  2   1   &
ATD  SH    *   16  2   2   &
ATD  S     *   16  2   & 
ATD  SO    *   16  4   & 
ATD  LP   *    0   &
ATD  DU  &
--------------------------------------------------------------------------------------------
============================================================================================




============================================================================================
			Field descriptions
============================================================================================
(1)  ATD, which stands for atom type defination, ATD should always in the first three columns 
(2)  Atom type name, can be letters or numbers   
(3)  Residue names, which means this description is only applied to atoms in special residues
(4)  Atomic number 
(5)  Number of attached atoms 
(6)  Number of attached hydrogen atoms
(7)  For hydrogen, number of the electron-withdrawal atoms connected to the atom that the 
     hydrogen attached
(8)  atomic property
(9)  Chemical enviornment definations


============================================================================================
			Specific symbols
============================================================================================
*  Ignore this field
&  End of defination 
.  "or" operation in the ring and aromatity descriptions 


============================================================================================
			Predefined words
============================================================================================
EW   Electron-withdraw atom
AA   Amino acid residue
NA   Nucleric acid
BIO  AA + NA

AR1  Pure aromatic atom (benzene and pyridine)
AR2  Atom in a planar ring, usually the ring has two continous single bonds
AR3  Atom in a planar ring, which has one or several double bonds formed between outside atoms
     and ring atoms
AR4  Atom other than AR1, AR2, AR3 and AR5. 
AR5  Pure aliphatic atom in a ring, which is made of sp3 carbon

RG   Ring (from 3-membered to nine-membered)
RG3  3-membered ring 
RG4  4-membered ring 
RG5  5-membered ring 
RG6  6-membered ring 
RG7  7-membered ring 
RG8  8-membered ring 
RG9  9-membered ring 
NG   non-ring atom 

SB   Single bond
DB   Double bond
TB   Triple bond
AB   Aromatic bond
sb   Single bond, including aromatic single
db   Double bond, including aromatic double
tb   Triple bond
 
============================================================================================
			Miscellaneous
============================================================================================
1. maximum line length is 500 characters
2. no space in the atomic property string
3. no space in the chemical environment string 
4. no filed missing before &
5. the defination order is crucial, special atom types should defined before the more general 
   ones
6. Bonds in COO- and -NO2 are considered as double bonds
